CellProfiler 2.1.1 seems to have stopped communicating fully with ImageJ in the execution of its RunImageJ module.
I have a simple pipeline and the RunImageJ module runs the Process…Enhance Contrast command. I have it configured to take as input the image from the previous item, then save the current output image for use in an ensuing module. For a time this was working, then it simply stopped integrating.
The input image is opened in ImageJ, the Enhance Contrast dialog is presented, and when it is dismissed the contrast is adjusted as expected. However, the CellProfiler dialog for the RunImageJ step says “No input image”. The “input” image for the ensuing module is identical to the input to the RunImageJ module, as though nothing at all had been done in ImageJ. The behavior is almost identical when using a beanshell macro. There are no errors in the CellProfiler console window, and the memory utilization for the worker process never rises above 300M.
Has anybody seen anything like this? Is there any deeper logging available other than the console window that might shed some light on what’s going on under the hood?